maegatk maegatk-indel: command not found...

Hi,

I was wondering the relationship between maegatk and maegatk-indel, is the output of the former the input of the latter?

In addition, after installing this package by 'pip3 install maegatk' ,I can use maegatk, but cannot use maegatk-indel (bash: maegatk-indel: command not found...). What should I do to make it work?

Thank you very much!

May 19 '22 21:05 zjy0419

@vincent6liu would you mind commenting here?

May 23 '22 06:05 caleblareau

Same installation issue here - 'maegatk-indel: command not found'. Seems that the PyPi package is not up-to-date. When I clone from github I and try to install from the clone I get (using python 3.8): ` $ pip install -e maegatk Obtaining file:///home/peter/git/maegatk Preparing metadata (setup.py) ... error error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [30 lines of output] Traceback (most recent call last): File "", line 2, in File "", line 34, in File "/home/peter/git/maegatk/setup.py", line 8, in setup( File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/init.py", line 107, in setup _install_setup_requires(attrs) File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/init.py", line 75, in _install_setup_requires dist = MinimalDistribution(attrs) File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/init.py", line 57, in init super().init(filtered) File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/dist.py", line 486, in init for ep in metadata.entry_points(group='distutils.setup_keywords'): File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/_vendor/importlib_metadata/init.py", line 856, in entry_points return EntryPoints(eps).select(**params) File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/_vendor/importlib_metadata/init.py", line 853, in eps = itertools.chain.from_iterable( File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/_vendor/importlib_metadata/_itertools.py", line 16, in unique_everseen k = key(element) File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/_vendor/importlib_metadata/_py39compat.py", line 18, in normalized_name return dist._normalized_name File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/_vendor/importlib_metadata/init.py", line 778, in _normalized_name or super()._normalized_name File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/_vendor/importlib_metadata/init.py", line 445, in normalized_name return Prepared.normalize(self.name) File "/home/peter/miniconda3/lib/python3.8/site-packages/setuptools/vendor/importlib_metadata/init.py", line 700, in normalize return re.sub(r"[-.]+", "-", name).lower().replace('-', '') File "/home/peter/miniconda3/lib/python3.8/re.py", line 210, in sub return _compile(pattern, flags).sub(repl, string, count) TypeError: expected string or bytes-like object [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed

× Encountered error while generating package metadata. ╰─> See above for output.

note: This is an issue with the package mentioned above, not pip. hint: See above for details.`

Mar 10 '23 11:03 pl-ki

I was able to clone the repo and install maegatk-indel via pip install -e . for a new version of python:

python --version
Python 3.11.6

maegatk-indel --help
Usage: maegatk-indel [OPTIONS]

  maegatk: a Maester genome toolkit.

  INDEL calling

I'm not sure the best way to proceed here at the moment...

Jan 16 '24 14:01 caleblareau

I have the same issue. I can run maegatk successfully at python 3.6.8, with snakemake 3.13.3 but maegatk-indel is not available. Then in the new env, maegatk-indel is available under python 3.11.10, but snakemake 8.25.3 give me the error when running maegatk that, snakemake: error: unrecognized arguments: --stats which snakemake should I use then to be compatible with python 3.11 and also support --stats argument?

Nov 22 '24 16:11 amberqiong

I have the same issue. I can run maegatk successfully at python 3.6.8, with snakemake 3.13.3 but maegatk-indel is not available. Then in the new env, maegatk-indel is available under python 3.11.10, but snakemake 8.25.3 give me the error when running maegatk that, snakemake: error: unrecognized arguments: --stats which snakemake should I use then to be compatible with python 3.11 and also support --stats argument?

Tested. Snakemake 7.24.2 works.

python --version Python 3.11.10 snakemake --version 7.24.2

Nov 25 '24 14:11 amberqiong